Murray Patterson

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 77

Top Topics

International Symposium

Feature Generation

Sequence Classification

Machine Learning

Top Venues

J. Comput. Biol.

Medical Biol. Eng. Comput.

Publications

Taslim Murad, Sarwan Ali, Murray Patterson
Weighted Chaos Game Representation for Molecular Sequence Classification. PKDD (4) (2024)
Sarwan Ali, Haris Mansoor, Prakash Chourasia, Yasir Ali, Murray Patterson
Gaussian Beltrami-Klein Model for Protein Sequence Classification: A Hyperbolic Approach. ISBRA (1) (2024)
Sarwan Ali, Prakash Chourasia, Murray Patterson
Expanding Chemical Representation with k-mers and Fragment-based Fingerprints for Molecular Fingerprinting. CoRR (2024)
Sarwan Ali, Tamkanat E. Ali, Prakash Chourasia, Murray Patterson
A Universal Non-parametric Approach for Improved Molecular Sequence Analysis. PKDD (4) (2024)
Zahra Tayebi, Sarwan Ali, Taslim Murad, Imdadullah Khan, Murray Patterson
PseAAC2Vec protein encoding for TCR protein sequence classification. Comput. Biol. Medicine 170 (2024)
Murray Patterson
19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023). J. Comput. Biol. 31 (6) (2024)
Sarwan Ali, Tamkanat E. Ali, Taslim Murad, Haris Mansoor, Murray Patterson
Molecular sequence classification using efficient kernel based embedding. Inf. Sci. 679 (2024)
Sarwan Ali, Tamkanat E. Ali, Prakash Chourasia, Murray Patterson
A Universal Non-Parametric Approach For Improved Molecular Sequence Analysis. CoRR (2024)
Sarwan Ali, Prakash Chourasia, Murray Patterson
From PDB files to protein features: a comparative analysis of PDB bind and STCRDAB datasets. Medical Biol. Eng. Comput. 62 (8) (2024)
Taslim Murad, Sarwan Ali, Murray Patterson
Exploring The Potential Of GANs In Biological Sequence Analysis. CoRR (2023)
Sarwan Ali, Babatunde Bello, Prakash Chourasia, Ria Thazhe Punathil, Pin-Yu Chen, Imdadullah Khan, Murray Patterson
Counterfactually Guided Policy Transfer in Clinical Settings. CHIL (2023)
Taslim Murad, Sarwan Ali, Imdadullah Khan, Murray Patterson
Spike2CGR: an efficient method for spike sequence classification using chaos game representation. Mach. Learn. 112 (10) (2023)
Taslim Murad, Sarwan Ali, Prakash Chourasia, Haris Mansoor, Murray Patterson
Circular Arc Length-Based Kernel Matrix For Protein Sequence Classification. BigData (2023)
Zahra Tayebi, Akshay Juyal, Alexander Zelikovsky, Murray Patterson
Simulating Tumor Evolution from scDNA-Seq as an Accumulation of both SNVs and CNAs. ISBRA (2023)
Sarwan Ali, Taslim Murad, Murray Patterson
PCD2Vec: A Poisson Correction Distance-Based Approach for Viral Host Classification. CoRR (2023)
Sarwan Ali, Pin-Yu Chen, Murray Patterson
Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences. ISBRA (2023)
Sarwan Ali, Prakash Chourasia, Murray Patterson
When Biology has Chemistry: Solubility And Drug Subcategory Prediction using SMILES Strings. Tiny Papers @ ICLR (2023)
Prakash Chourasia, Zahra Tayebi, Sarwan Ali, Murray Patterson
Empowering Pandemic Response with Federated Learning for Protein Sequence Data Analysis. IJCNN (2023)
Mansoor Ahmed, Usama Sardar, Sarwan Ali, Shafiq Alam, Murray Patterson, Imdadullah Khan
Robust Brain Age Estimation via Regression Models and MRI-Derived Features. ICCCI (CCIS Volume) (2023)
Sarwan Ali, Haris Mansoor, Prakash Chourasia, Murray Patterson
Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification. ISBRA (2023)
Sarwan Ali, Taslim Murad, Murray Patterson
PCD2Vec: A Poisson Correction Distance Based Approach for Viral Host Classification. IJCNN (2023)
Mansoor Ahmed, Usama Sardar, Sarwan Ali, Shafiq Alam, Murray Patterson, Imdadullah Khan
Robust Brain Age Estimation via Regression Models and MRI-derived Features. CoRR (2023)
Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson
Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data. J. Comput. Biol. 30 (4) (2023)
Sarwan Ali, Bikram Sahoo, Muhammad Asad Khan, Alexander Zelikovsky, Imdadullah Khan, Murray Patterson
Efficient Approximate Kernel Based Spike Sequence Classification. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Sarwan Ali, Prakash Chourasia, Zahra Tayebi, Babatunde Bello, Murray Patterson
ViralVectors: compact and scalable alignment-free virome feature generation. Medical Biol. Eng. Comput. 61 (10) (2023)
Sarwan Ali, Prakash Chourasia, Zahra Tayebi, Babatunde Bello, Murray Patterson
ViralVectors: Compact and Scalable Alignment-free Virome Feature Generation. CoRR (2023)
Sarwan Ali, Usama Sardar, Murray Patterson, Imdadullah Khan
BioSequence2Vec: Efficient Embedding Generation For Biological Sequences. CoRR (2023)
Prakash Chourasia, Taslim Murad, Sarwan Ali, Murray Patterson
Enhancing t-SNE Performance for Biological Sequencing Data Through Kernel Selection. ISBRA (2023)
Sarwan Ali, Usama Sardar, Imdadullah Khan, Murray Patterson
Efficient Sequence Embedding for SARS-CoV-2 Variants Classification. ISBRA (2023)
Usama Sardar, Sarwan Ali, Muhammad Sohaib Ayub, Muhammad Shoaib, Khurram Bashir, Imdadullah Khan, Murray Patterson
Sequence-Based Nanobody-Antigen Binding Prediction. ISBRA (2023)
Zahra Tayebi, Sarwan Ali, Prakash Chourasia, Taslim Murad, Murray Patterson
T Cell Receptor Protein Sequences and Sparse Coding: A Novel Approach to Cancer Classification. CoRR (2023)
Sarwan Ali, Usama Sardar, Murray Patterson, Imdadullah Khan
BioSequence2Vec: Efficient Embedding Generation for Biological Sequences. PAKDD (2) (2023)
Sarwan Ali, Prakash Chourasia, Murray Patterson
PDB2Vec: Using 3D Structural Information for Improved Protein Analysis. ISBRA (2023)
Prakash Chourasia, Taslim Murad, Zahra Tayebi, Sarwan Ali, Imdadullah Khan, Murray Patterson
Efficient Classification of SARS-CoV-2 Spike Sequences Using Federated Learning. CoRR (2023)
Usama Sardar, Sarwan Ali, Muhammad Sohaib Ayub, Muhammad Shoaib, Khurram Bashir, Imdadullah Khan, Murray Patterson
Sequence-Based Nanobody-Antigen Binding Prediction. CoRR (2023)
Sarwan Ali, Babatunde Bello, Zahra Tayebi, Murray Patterson
Characterizing SARS-CoV-2 Spike Sequences Based on Geographical Location. J. Comput. Biol. 30 (4) (2023)
Sarwan Ali, Babatunde Bello, Prakash Chourasia, Ria Thazhe Punathil, Pin-Yu Chen, Imdadullah Khan, Murray Patterson
Virus2Vec: Viral Sequence Classification Using Machine Learning. CoRR (2023)
Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021). J. Comput. Biol. 30 (4) (2023)
Zahra Tayebi, Sarwan Ali, Prakash Chourasia, Taslim Murad, Murray Patterson
T Cell Receptor Protein Sequences and Sparse Coding: A Novel Approach to Cancer Classification. ICONIP (10) (2023)
Taslim Murad, Sarwan Ali, Murray Patterson
A New Direction in Membranolytic Anticancer Peptides classification: Combining Spaced k-mers with Chaos Game Representation. INNS DLIA@IJCNN (2023)
Sarwan Ali, Prakash Chourasia, Murray Patterson
Anderson Acceleration for Bioinformatics-Based Machine Learning. KDH@IJCAI (2023)
Sarwan Ali, Prakash Chourasia, Murray Patterson
Anderson Acceleration For Bioinformatics-Based Machine Learning. CoRR (2023)
Sarwan Ali, Yijing Zhou, Murray Patterson
Efficient analysis of COVID-19 clinical data using machine learning models. Medical Biol. Eng. Comput. 60 (7) (2022)
Prakash Chourasia, Sarwan Ali, Murray Patterson
Informative Initialization and Kernel Selection Improves t-SNE for Biological Sequences. CoRR (2022)
Sarwan Ali, Taslim Murad, Prakash Chourasia, Murray Patterson
Spike2Signal: Classifying Coronavirus Spike Sequences with Deep Learning. BigDataService (2022)
Sarwan Ali, Bikram Sahoo, Muhammad Asad Khan, Alexander Zelikovsky, Imdadullah Khan, Murray Patterson
Efficient Approximate Kernel Based Spike Sequence Classification. CoRR (2022)
Prakash Chourasia, Sarwan Ali, Murray Patterson
Informative Initialization and Kernel Selection Improves t-SNE for Biological Sequences. Big Data (2022)
Taslim Murad, Prakash Chourasia, Sarwan Ali, Murray Patterson
Hashing2Vec: Fast Embedding Generation for SARS-CoV-2 Spike Sequence Classification. ACML (2022)
Sarwan Ali, Taslim Murad, Murray Patterson
PSSM2Vec: A Compact Alignment-Free Embedding Approach for Coronavirus Spike Sequence Classification. ICONIP (7) (2022)
Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson
Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data. CoRR (2022)
Kaustubh Khandai, Cristian Navarro-Martinez, Brendan Smith, Rebecca Buonopane, S. Ashley Byun, Murray Patterson
Determining Significant Correlation Between Pairs of Extant Characters in a Small Parsimony Framework. J. Comput. Biol. 29 (10) (2022)
Sarwan Ali, Babatunde Bello, Prakash Chourasia, Ria Thazhe Punathil, Yijing Zhou, Murray Patterson
PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences. CoRR (2022)
Sarwan Ali, Bikram Sahoo, Alexander Zelikovskiy, Pin-Yu Chen, Murray Patterson
Benchmarking Machine Learning Robustness in Covid-19 Genome Sequence Classification. CoRR (2022)
Sarwan Ali, Babatunde Bello, Murray Patterson
Classifying COVID-19 Spike Sequences from Geographic Location Using Deep Learning. CoRR (2021)
Simone Ciccolella, Murray Patterson, Paola Bonizzoni, Gianluca Della Vedova
Effective Clustering for Single Cell Sequencing Cancer Data. IEEE J. Biomed. Health Informatics 25 (11) (2021)
Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. Bioinform. 37 (3) (2021)
Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson
Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data. ICCABS (2021)
Sarwan Ali, Bikram Sahoo, Naimat Ullah, Alexander Zelikovskiy, Murray Patterson, Imdadullah Khan
A k-mer Based Approach for SARS-CoV-2 Variant Identification. ISBRA (2021)
Zahra Tayebi, Sarwan Ali, Murray Patterson
Robust Representation and Efficient Feature Selection Allows for Effective Clustering of SARS-CoV-2 Variants. CoRR (2021)
Sarwan Ali, Murray Patterson
Spike2Vec: An Efficient and Scalable Embedding Approach for COVID-19 Spike Sequences. IEEE BigData (2021)
Sarwan Ali, Murray Patterson
Spike2Vec: An Efficient and Scalable Embedding Approach for COVID-19 Spike Sequences. CoRR (2021)
Sarwan Ali, Yijing Zhou, Murray Patterson
Efficient Analysis of COVID-19 Clinical Data using Machine Learning Models. CoRR (2021)
Zahra Tayebi, Sarwan Ali, Murray Patterson
Robust Representation and Efficient Feature Selection Allows for Effective Clustering of SARS-CoV-2 Variants. Algorithms 14 (12) (2021)
Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering. J. Comput. Biol. 28 (11) (2021)
Brendan Smith, Cristian Navarro-Martinez, Rebecca Buonopane, S. Ashley Byun, Murray Patterson
Correlated Evolution in the Small Parsimony Framework. ISBRA (2021)
Sarwan Ali, Tamkanat E. Ali, Muhammad Asad Khan, Imdadullah Khan, Murray Patterson
Effective and scalable clustering of SARS-CoV-2 sequences. CoRR (2021)
Sarwan Ali, Bikram Sahoo, Naimat Ullah, Alexander Zelikovskiy, Murray Patterson, Imdadullah Khan
A k-mer Based Approach for SARS-CoV-2 Variant Identification. CoRR (2021)
Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson
Simpler and Faster Development of Tumor Phylogeny Pipelines. J. Comput. Biol. 28 (11) (2021)
Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
Clustering Based Identification of SARS-CoV-2 Subtypes. ICCABS (2020)
Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson
A rearrangement distance for fully-labelled trees. CoRR (2019)
Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson
A Rearrangement Distance for Fully-Labelled Trees. CPM (2019)
Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni
Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era. Quant. Biol. 7 (4) (2019)
Simone Ciccolella, Mauricio Soto Gomez, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. ICCABS (2018)
Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinform. 19 (1) (2018)
Gianluca Della Vedova, Murray Patterson, Raffaella Rizzi, Mauricio Soto Gomez
Character-Based Phylogeny Construction and Its Application to Tumor Evolution. CiE (2017)
Andrea Bracciali, Marco Aldinucci, Murray Patterson, Tobias Marschall, Nadia Pisanti, Ivan Merelli, Massimo Torquati
PWHATSHAP: efficient haplotyping for future generation sequencing. BMC Bioinform. 17 (S-11) (2016)
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. J. Comput. Biol. 22 (6) (2015)
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth
WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. RECOMB (2014)
Marco Aldinucci, Andrea Bracciali, Tobias Marschall, Murray Patterson, Nadia Pisanti, Massimo Torquati
High-Performance Haplotype Assembly. CIBB (2014)
Ján Manuch, Murray Patterson, Roland Wittler, Cédric Chauve, Eric Tannier
Linearization of ancestral multichromosomal genomes. CTW (2013)
Cédric Chauve, Murray Patterson, Ashok Rajaraman
Hypergraph covering problems motivated by genome assembly questions. CoRR (2013)
Murray Patterson, Gergely J. Szöllosi, Vincent Daubin, Eric Tannier
Lateral gene transfer, rearrangement, reconciliation. BMC Bioinform. 14 (S-15) (2013)
Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau
Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinform. 14 (S-15) (2013)
Cédric Chauve, Murray Patterson, Ashok Rajaraman
Hypergraph Covering Problems Motivated by Genome Assembly Questions. IWOCA (2013)
Ján Manuch, Murray Patterson, Roland Wittler, Cédric Chauve, Eric Tannier
Linearization of ancestral multichromosomal genomes. BMC Bioinform. 13 (S-19) (2012)
Ján Manuch, Murray Patterson, Cédric Chauve
Hardness results on the gapped consecutive-ones property problem. Discret. Appl. Math. 160 (18) (2012)
Ján Manuch, Murray Patterson
The Complexity of the Gapped Consecutive-Ones Property Problem for Matrices of Bounded Maximum Degree. J. Comput. Biol. 18 (9) (2011)
Roland Wittler, Ján Manuch, Murray Patterson, Jens Stoye
Consistency of Sequence-Based Gene Clusters. J. Comput. Biol. 18 (9) (2011)
Ján Manuch, Murray Patterson, Arvind Gupta
Towards a Characterisation of the Generalised Cladistic Character Compatibility Problem for Non-branching Character Trees. ISBRA (2011)
Cédric Chauve, Ján Manuch, Murray Patterson, Roland Wittler
Tractability Results for the Consecutive-Ones Property with Multiplicity. CPM (2011)
Ján Manuch, Murray Patterson
The Complexity of the Gapped Consecutive-Ones Property Problem for Matrices of Bounded Maximum Degree. RECOMB-CG (2010)
Ján Manuch, Murray Patterson, Sheung-Hung Poon, Chris Thachuk
Complexity of Finding Non-Planar Rectilinear Drawings of Graphs. Graph Drawing (2010)
Cédric Chauve, Ján Manuch, Murray Patterson
Hardness Results for the Gapped Consecutive-Ones Property CoRR (2009)
Cédric Chauve, Ján Manuch, Murray Patterson
On the Gapped Consecutive-Ones Property. Electron. Notes Discret. Math. 34 (2009)
Ján Manuch, Murray Patterson, Arvind Gupta
On the Generalised Character Compatibility Problem for Non-branching Character Trees. COCOON (2009)
Murray Patterson, Yongmei Liu, Eugenia Ternovska, Arvind Gupta
Grounding for Model Expansion in k-Guarded Formulas with Inductive Definitions. IJCAI (2007)
Thomas Bruckner, Robbie Morrison, Chris Handley, Murray Patterson
: Overview and Application to Policy Development. Ann. Oper. Res. 121 (1-4) (2003)